Synthesis of sulfurized oligonucleotides

ABSTRACT

Methods for the formation of sulfurized oligonucleotides are provided. The methods allow for the formation of phosphorothioate linkages in the oligonucleotides or derivatives, without the need for complex solvent mixtures and repeated washing or solvent changes. Oligonucleotides having from about 8, and up to about 50, nucleotides can be sulfurized according to the methods of the invention with higher yields than have been previously reported.

CROSS-REFERENCES TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No.10/181,200, filed on Dec. 12, 2002, issued as U.S. Pat. No. 7,227,015 onJun. 5, 2007, which is the U.S. National Stage of InternationalApplication No. PCT/US01/00715, filed Jan. 10, 2001 and published asWO01/51502, which is a continuation of U.S. application Ser. No.09/481,486, filed Jan. 11, 2000 and now U.S. Pat. No. 6,242,591, each ofwhich are hereby incorporated by reference in its entirety.

FIELD OF THE INVENTION

The present invention is directed to methods for synthesizing sulfurizedoligonucleotides and analogs thereof. The methods employ a phenylacetyldisulfide reagent in a simplified solvent system and produceoligonucleotides having phosphorothioate groups with great efficiencyand improved yields.

BACKGROUND OF THE INVENTION

Modified oligonucleotides are of great value in molecular biologicalresearch and in applications such as anti-viral therapy. Modifiedoligonucleotides which can block RNA translation, and are nucleaseresistant, are useful as antisense reagents. Sulfurizedoligonucleotides, which contain phosphorothioate (P—S) linkages, are ofinterest in these areas. Phosphorothioate-containing oligonucleotidesare also useful in determining the stereochemical pathways of certainenzymes which recognize nucleic acids.

Standard techniques for sulfurization of phosphorous-containingcompounds have been applied to the synthesis of sulfurizedoligonucleotides. Examples of sulfurization reagents which have beenused to synthesize oligonucleotides containing phosphorothioate bondsinclude elemental sulfur, dibenzoyl tetrasulfide,3-H-1,2-benzidithiol-3-one 1,1-dioxide (also known as Beaucage reagent),tetraethylthiuram disulfide (TETD), and bis(O,O-diisopropoxyphosphinothioyl) disulfide (known as Stec reagent). Most of the knownsulfurization reagents, however, have one or more significantdisadvantages.

Elemental sulfur presents problems and is not suitable for automationbecause of its insolubility in most organic solvents. Furthermore,carbon disulfide, a preferred source of sulfur, has undesirablevolatility and an undesirably low flash point. Unwanted side productsare often observed with the use of dibenzoyl tetrasulfide. Beaucagereagent, while a relatively efficient sulfurization reagent, isdifficult to synthesize and not particularly stable. Furthermore, use ofBeaucage reagent forms a secondary reaction product which is a potentoxidizing agent. (R. P. Iyer et al., J. Am. Chem. Soc. 112, pp.1253–1254 (1990); R. P. Iyer et al., J. Org. Chem. 55, 4693–4699(1990)). This can further lead to unwanted side products which can bedifficult to separate from the desired reaction product.Tetraethylthiuram disulfide, while relatively inexpensive and stable,has a sulfurization reaction rate which can be undesirable slow.

A method for producing a phosphorothioate ester by reaction of aphosphite ester with an acyl disulfide is disclosed in Dutch patentapplication No. 8902521. The disclosed method is applied to a purifiedphosphotriester dimer utilizing solution phase chemistry. The method istime and labor intensive in that it was only shown to work in a complexscheme which involved carrying out the first stage of synthesis(formation of a phosphite) in acetonitrile, removing the acetonitrile,purifying the intermediate phosphotriester, and proceeding with thesulfurization in a solvent mixture of dichloroethane (DCE) and2,4,6-collidine. Furthermore, the method was demonstrated only with adinucleotide. There was no suggestion that the Dutch method could beemployed with larger nucleic acid structures, that the same could employa common solvent throughout all steps of synthesis, that improved yieldscould be obtained, or that the method could be adapted for conventionalautomated synthesis without extensive modification of the scheme ofautomation. Although acetonitrile is mentioned as one of severalpossible solvents, utility of the method for carrying out all steps ofthe synthesis in acetonitrile as a common solvent was not demonstrated.While other publications (Kamer et al., Tetrahedron Letters 30(48), pp.6757–6760(1989); Roelen et al., Rech. Trav. Chim. Pays-Bas 110, pp.325–331 (1991)) show sulfurization of oligomers having up to 6nucleotides, the foregoing shortcomings are not overcome by the methodsdisclosed in these references.

Thus, there remains a need for improved methods and reagents forpreparing sulfur-containing phosphorous groups, such as phosphorothioatelinkages, in oligonucleotides and other organic compounds. The presentinvention is directed to these, as well as other, important ends.

SUMMARY OF THE INVENTION

The present invention provides methods for synthesis of phosphorothioateoligonucleotides with improved yields as compared to those obtained withprior methods. Moreover, the present methods are useful for thesynthesis of not only phosphorothioate oligonucleotides havingrelatively large numbers of nucleotide and/or nucleoside units therein,e.g. from about 6 to about 50, and even more, and particularly fromabout 8 to about 30 nucleotide and/or nucleoside units. The methods ofthe present invention employ a greatly simplified solvent system, onewhich is compatible with automated synthetic reaction schemes andcommercial synthesizers. The resulting improvement in syntheticopportunities permits wide application of the present methods throughoutnucleic acid chemistry.

One aspect of the present invention discloses methods for synthesizingphosphorothioate oligonucleotides, comprising the steps ofphosphitylating a 5′-hydroxyl moiety of a nucleotide, nucleoside,oligonucleotide or an oligonucleoside, and contacting the resultantphosphite intermediate with a phenylacetyl disulfide in the presence ofa solvent system that includes acetonitrile for a time sufficient toeffect the formation of a phosphorothioate functional group.Phosphorothioate oligonucleotides having a predetermined length andsequence can be prepared by repeating the phosphitylating and oxidizingsteps.

In further aspects of the present invention, methods for the synthesisof phosphorothioate oligonucleotide analogs are disclosed, comprisingthe substitution of modified nucleotides, nucleosides, oligonucleotidesand oligonucleosides for nucleotides, nucleosides, oligonucleotides oroligonucleosides. Modifications to nucleotides, nucleosides,oligonucleotides and oligonucleosides are well known in the art. As usedherein the term “phosphorothioate oligonucleotide” is meant to includeanalogs as defined above.

The term “phosphite moiety” as used herein is meant to include phosphitemoieties within nucleosides, nucleotides, oligonucleosides andoligonucleotides. In a preferred embodiment, phosphite moieties are inan activated state such as a dimethoxytritylphosphoramidite. The terms“nucleotide, nucleoside, oligonucleotide or an oligonucleoside” as usedherein are intended to include both naturally occurring species andnon-naturally occurring or modified species as is known to those skilledin the art. Common modifications include sugar modifications such as 2′modifications and base modifications or the use of substitute bases.When an oligonucleotide or modified oligonucleotide is used as thephosphite moiety, modified linkages as is commonly known in the art mayalso be present.

The present methods have demonstrated lower levels of impurities andhigher yields compared to when DCE is used as a solvent for theoxidation step. The present methods have also shown, unexpectedly, thatyields of about 99% can be obtained in acetonitrile/picoline.Acetonitrile/picoline is entirely compatible with automated synthesiswithout extensive modification to the synthetic routine, so that thepresent methods can be advantageously used in an automated synthesizer.For example, extensive washes are not required because a single solventor mixture having a common solvent is used in all automated syntheticsteps. Thus, solvent removal and wash steps can be eliminated. It hasalso been surprisingly discovered that high yields can be achieved whensynthesizing phosphorothioate oligonucleotides or oligonucleotideanalogs having from about 8 nucleotides and up to about 30 nucleotides.

Suitable solvent systems for use in the oxidation of the phosphiteintermediate of the present invention include mixtures of two or moresolvents. Preferably a mixture of an aprotic solvent with a protic orbasic solvent. Preferred solvent mixtures include acetonitrile/picolineand acetonitrile/lutidine. Suitable aprotic solvents include pyridineand hindered pyridines such as lutidine, collidine, and picoline.Solvent mixtures can include, for example, two solvents such asacetonitrile and picoline, or acetonitrile and lutidine, in a volumeratio of from about 1:1.5 to about 1.5:1, preferably about 1:1.

Sulfurization (oxidation utilizing a sulfurizing reagent), according tothe methods of the present invention, is carried out by contacting anoligonucleotide or analog with an acetyl disulfide for a time sufficientto effect formation of a phosphorothioate functional group. Preferredreagents include phenylacetyl disulfide, arylacetyl disulfide, and arylsubstituted phenylacetyl disulfides.

Contacting the phosphite moiety with acetyl disulfide can be done usingprocedures and equipment known to those skilled in the art. For example,a glass reactor such as a flask can be suitably employed. Preferably,solid phase synthesis procedures are employed, and a solid support suchas controlled pore glass. Even more preferably, the methods of thepresent invention can be carried out using automatic DNA synthesizers.Suitable solid phase techniques, including automated synthesistechniques, are described in F. Eckstein (ed.), Oligonucleotides andAnalogues, a Practical Approach. Oxford University Press, New York(1991).

The methods of the present invention can be suitably carried out at roomtemperature. “Room temperature” includes ambient temperatures from about20° C. to about 30° C. Reaction times are on the order of minutes, suchas, for example, 2, 3, 4, or 5 minutes, or even as short as about 100seconds.

Generally, methods of the present invention include phosphitylating the5′-hydroxyl group of a nucleic acid moiety to form a phosphiteintermediate and oxidizing the phosphite intermediate with an acetyldisulfide for a time sufficient to effect conversion of the phosphiteintermediate to a phosphorothioate. The phosphite intermediate can be,for example, a phosphite linked dinucleotide, or an oligonucleotide oroligonucleoside having at least one phosphite linkage therein. Thephosphitylation and oxidation steps of the method are both performed ina system that includes acetonitrile. Repetition of the phosphitylationand oxidation steps will give the phosphorothioate oligonucleotidehaving a predetermined length. Reaction progress can be monitored bywell-known techniques such as proton or ³¹P NMR. The reaction productcan be treated with a base such as, for example, ammonium hydroxidesolution at a concentration of about 30 percent. The desired product canbe readily isolated by, for example, standard filtration techniques.

The following examples are merely illustrative of the present inventionand should not be considered limiting of the scope of the invention inany way. These examples and equivalents thereof will become moreapparent to those skilled in the art in light of the present disclosureand the accompanying claims.

EXAMPLE 1 Synthesis of 5′-TTTTTTT′-3′ phosphorothioate heptamer

50 milligram (2 μmole) of 5′-O-dimethoxytritylthymidine bound to CPG(controlled pore glass) through an ester linkage is taken up in a glassreactor, and a dichloromethane solution of 2% dichloroacetic acid(volume/volume) is added to deprotect the 5′ hydroxyl group. The productis washed with acetonitrile. Then, a 0.2 M solution of5′-O-(4,4′-dimethoxytrityl)thymidine-3′-O-(2-cyanoethylN,N-diisopropylphosphoramidite) in acetonitrile and a 0.4 M solution of1H-tetrazole in acetonitrile is added, and allowed to react at roomtemperature for 5 minutes. The product is washed with acetonitrile, andthen a 0.2 M solution of phenylacetyl disulfide inacetonitrile:3-picoline (1:1 v/v) is added and allowed to react at roomtemperature for 3 minutes. This sulfurization step is repeated one moretime for 3 minutes. The support is washed with acetonitrile, and then asolution of acetic anhydride/lutidine/THF (1:1:8), and N-methylimidazole/THF is added to cap any unreacted 5′-hydroxyl group. Theproduct is washed with acetonitrile.

This complete cycle is repeated five more times to produce thecompletely protected thymidine heptamer. The carrier containing thecompound is treated with 30% aqueous ammonium hydroxide solution for 90minutes at room temperature. The aqueous solution is filtered, andconcentrated under reduced pressure to give a phosphorothioate heptamer,TTTTTTT.

EXAMPLE 2 Synthesis of 5′-d(GACT)-3′ phosphorothioate tetramer

50 milligram (2×10⁻⁶ mole (2 μmole)) of 5′-O-dimethoxytritylthymidinebound to CPG (controlled pore glass) through an ester linkage is takenup in a glass reactor, and a dichloromethane solution of 2%dichloroacetic acid (volume/volume) is added to deprotect the5′-hydroxyl group. The product is washed with acetonitrile. Then, a 0.2M solution of 5′-O-(4,4′-dimethoxytrityl)thymidine-3′-O-(2-cyanoethylN,N-diisopropylphosphoramidite) in acetonitrile and a 0.4 M solution of1H-tetrazole in acetonitrile is added, and allowed to react at roomtemperature for 5 minutes. The product is washed with acetonitrile, andthen a 0.2 M solution of phenylacetyl disulfide inacetonitrile:3-picoline (1:1 v/v) is added and allowed to react at roomtemperature for 3 minutes. This sulfurization step is repeated one moretime for 3 minutes. The support is washed with acetonitrile and then asolution of acetic anhydride/lutidine/THF (1:1:8), and N-methylimidazole/THF is added to cap the unreacted 5′-hydroxyl group. Theproduct is washed with acetonitrile.

A solution of 2% dichloroacetic acid (volume/volume) is added todeprotect the 5′-hydroxyl group The product is washed with acetonitrile.Then, a 0.2 M solution of N⁴-benzoyl-5′-O-(4,4′dimethoxytrityl)-2′-deoxycytidine-3′-O-(2-cyanoethyl N,N′diisopropylphosphoramidite) in acetonitrile and a 0.4 M solution of 1H-tetrazole inacetonitrile is added, and allowed to react at room temperature for 5minutes. The product is washed with acetonitrile, and then a 0.2 Msolution of phenylacetyl disulfide in acetonitrile:3 picoline (1:1 v/v)is added and allowed to react at room temperature for 3 minutes. Thissulfurization step is repeated one more time for 3 minutes. The supportis washed with acetonitrile and then a solution of aceticanhydride/lutidine/THF (1:1:8), and N-methyl imidazole/THF is added tocap any unreacted 5′-hydroxyl group. The product is washed withacetonitrile.

A solution of 2% dichloroacetic acid (volume/volume) is added todeprotect the 5′-hydroxyl group. The product is washed withacetonitrile. Then, a 0.2 M solution of N6-benzoyl-5′-O-(4,4′dimethoxytrityl)-2′-deoxyadenosine-3′-O-(2-cyanoethyl-N,N′diisopropylphosphoramidite) in anhydrous acetonitrile and a 0.4 Msolution of 1H-tetrazole in acetonitrile is added, and allowed to reactat room temperature for 5 minutes. The product is washed withacetonitrile, and then a 0.2 M solution of phenylacetyl disulfide inacetonitrile:3-picoline (1:1 v/v) is added and allowed to react at roomtemperature for 3 minutes. This sulfurization step is repeated one moretime for 3 minutes-The support is washed with acetonitrile and then asolution of acetic anhydride/lutidine/THF (1:1:8), and N-methylimidazole/THF is added to cap the unreacted 5′-hydroxyl group. Theproduct is washed with acetonitrile.

A solution of 2% dichloroacetic acid (volume/volume) is added todeprotect the 5′-hydroxyl group. The product is washed withacetonitrile. Then, a 0.2 M solution of N2-isobutyl-5′-O-4,4′dimethoxytrityl-deoxyguanosine-3′-O-(2-cyanoethyl N,N′ diisopropylphosphoramidite) in acetonitrile and a 0.4 M solution of 1H-tetrazole inacetonitrile is added, and allowed to react at room temperature for 5minutes. The product is washed with acetonitrile, and then a 0.2 Msolution of phenylacetyl disulfide in acetonitrile: 3 picoline (1:1 v/v)is added and allowed to react at room temperature for 3 minutes. Thissulfurization step is repeated one more time for 3 minutes. The supportis washed with acetonitrile and then a solution of aceticanhydride/lutidine/THF (1:1:8), and N-methyl imidazole/THF is added tocap any unreacted 5′-hydroxyl group. The product is washed withacetonitrile.

The carrier containing the compound is treated with 30% aqueousammnoniiun hydroxide solution for 90 minutes a: room temperature andthen incubated at 55° C. for 24 hour. The aqueous solution is filtered,concentrated under reduced pressure to give a phosphorothioate tetramerof 5′-dG-dA-dC-T-3′.

EXAMPLE 3 Synthesis of fully-modified5′-d(TCC-CGC-CTG-TGA-CAT-GCA-TT)-3′ phosphorothioate 20-mer <Seq. ID No.1>

The synthesis of the above sequence was performed on a PharmaciaOligoPilot II Synthesizer on a 620 μmole scale using the cyanoethylphosphoramidites and Pharmacia's primar support. Sulfurization wasperformed using a 0.2 M solution of phenylacetyl disulfide inacetonitrile:3-picoline (1:1 v/v) for 2 minutes. At the end ofsynthesis, the support was washed with acetonitrile, cleaved,deprotected and purified as has been previously illustrated above.

EXAMPLE 4 Synthesis of fully-modified 5′d(GCC-CAA-GCT-GGC-ATC-CGT-CA)-3′phosphorothioate 20-mer <Seq. ID No. 2>

The synthesis of the above sequence was performed on a PharmaciaOligoPilot II Synthesizer on a 620 μmole scale using the cyanoethylphosphoramidites and Pharmacia's primar support. Sulfurization wasperformed using a 0.2 M solution of phenylacetyl disulfide inacetonitrile:3-picoline (1:1 v/v) for 2 minutes-At the end of synthesis,the support was washed with acetonitrile, cleaved, deprotected andpurified as has been previously illustrated above.

EXAMPLE 5 Synthesis of fully-modified5′-d(GCG-TTT-GCT-CTT-CTT-CTT-GCG)-3′ phosphorothioate 21-mer <Seq. IDNo. 3>

The synthesis of the above sequence was performed on a PharmaciaOligoPilot II Synthesizer on a 620 μmole scale using the cyanoethylphosphoramidites and Pharmacia's primar support. Sulfurization wasperformed using a 0.2 M solution of phenylacetyl disulfide inacetonitrile:3-picoline (1:1 v/v) for 2 minutes. At the end ofsynthesis, the support was washed with acetonitrile, cleaved,deprotected and purified as has been previously illustrated above.

EXAMPLE 6 Synthesis of fully-modified 5′d(GTT-CTC-GCT-GGT-GAG-TTT-CA)-3′phosphorothioate 20-mer <Seq. ID No. 4>

The synthesis of the above sequence was performed on a PharmaciaOligoPilot II Synthesizer on a 620 μmole scale using the cyanoethylphosphoramidites and Pharmacia's primar support. Sulfurization wasperformed using a 0.2 M solution of phenylacetyl disulfide inacetonitrile:3-picoline (1:1 v/v) for 2 minutes. At the end ofsynthesis, the support was washed with acetonitrile, cleaved,deprotected and purified as has been previously illustrated above.

EXAMPLE 7 Synthesis of fully-modified5′d(TCC-CGC-CTG-TGA)-2′-methoxyethyl-(CAU-GCA-UU)-3′ phosphorothioate20-mer <Seq. ID No. 5>

The synthesis of the above sequence was performed on a Milligen 8800Synthesizer on a 282 μmole scale using the cyanoethyl phosphoramiditesand Pharmacia's primar support. Sulfurization was performed using a 0.4M solution of phenylacetyl disulfide in acetonitrile:3-picoline (1:1v/v) for 6 minutes. At the end of synthesis, the support was washed withacetonitrile, cleaved, deprotected and purified as has been previouslyillustrated above.

EXAMPLE 8 Synthesis of fully-modified 5′d(TCCGC-CTG-TGA)2′methoxyethyl-(CAU-GCA-UU)-3′ phosphorothioate 20-mer <Seq. ID No. 6>

The synthesis of the above sequence was performed on a PharmaciaOligoPilot II Synthesizer on a 250 μmole scale using the cyanoethylphosphoramidites and Pharmacia's primar support. Sulfurization wasperformed using a 0.4 M solution of phenylacetyl disulfide inacetonitrile:3-picoline (1:1 v/v) for 10 minutes. At the end ofsynthesis, the support was washed with acetonitrile, cleaved,deprotected and purified as has been previously illustrated above.

EXAMPLE 9 Synthesis of fully-modified5′-[2′-methoxyethyl(GCGUUUG)-d[CTCTTCT]-[2′-methoxyethyl-(UCUUGC)-dG-3′phosphorothioate 21-mer <Seq. ID No. 7>

The synthesis of the above sequence was performed on a PharmaciaOligoPilot II Synthesizer on a 250 μmole scale using the cyanoethylphosphoramidites and Pharmacia's primar support. Sulfurization wasperformed using a 0.4 M solution of phenylacetyl disulfide inacetonitrile:3-picoline (1-1 v/v) for 6 minutes. At the end ofsynthesis, the support was washed with acetonitrile, cleaved,deprotected and purified as has been previously illustrated above.

EXAMPLE 10 Synthesis of fully-modified5′-d(GCC-CAA-GCT-GGC)-2′-methoxyethyl-(AUC-CGU-CA)-3′ phosphorothioate20-mer <Seq. ID No. 8>

The synthesis of the above sequence was performed on a Milligen 8800Synthesizer on a 565 μmole scale using the cyanoethyl phosphoramiditesand Pharmacia's primar support. Sulfurization was performed using a 0.4M solution of phenylacetyl disulfide in acetonitrile:3-picoline (1:1v/v) for 6 minutes. At the end of synthesis, the support was washed withacetonitrile, cleaved, deprotected and purified as has been previouslyillustrated above.

EXAMPLE 11 Synthesis of fully-modified5′-d(GCC-CAA-GCT-GGC)-2′-methoxyethyl-(AUC-CGU-CA)-3′ phosphorothioate20-mer <Seq. ID No. 9>

The synthesis of the above sequence was performed on a PharmaciaOligoPilot II Synthesizer on a 680 μmole scale using the cyanoethylphosphoramidites and Pharmacia's primar support. Sulfurization wasperformed using a 0.4 M solution of phenylacetyl disulfide inacetonitrile:3-picoline (1:1 v/v) for 6 minutes. At the end ofsynthesis, the support was washed with acetonitrile, cleaved,deprotected and purified as has been previously illustrated above.

EXAMPLE 12 Synthesis of fully-modified5′-[2′-O-methoxyethyl-(TTT-TTT-TTT-TTT-TTT-TTT-TT)-3′ phosphorothioate20-mer <Seq. ID No. 10>

The synthesis of the above homo-pyrimidine sequence was performed on aPharmacia OligoPilot II synthesizer on an 180 μmole scale usingcyanoethyl phosphoramidite of5′-O-DMT-2′-O-methoxyethyl-5-methyluridine. Pharmacia's HL 30 primersupport loaded with 2′-O-methoxyethyl-5-methyluridine was used.Detritylation was performed using 3% dichloroacetic acid in toluene(volume/volume). Activation of phosphoramidite was done with a 0.45 Msolution of 1H-tetrazole in acetonitrile. Sulfurization was performedusing a 0.2 M solution of phenylacetyl disulfide inacetonitrile:3-picoline (1:1 v/v) for 2 minutes. At the end ofsynthesis, the support was treated with a solution oftriethylamine:acetonitrile (1:1, v/v) for 12 hours, support washed withacetonitrile, oligo cleaved, and deprotected with 33% aqueous ammoniumhydroxide at 55° C. for 12 hours, cooled, concentrated, and purified byreversed phase HPLC. All DMT fractions were combined, analyzed bycapillary gel electrophoresis, detritylated, precipitated andlyophilized to a powder. The stepwise sulfurization efficiency was foundto 99.6% based on ³¹P NMR (D₂O).

EXAMPLE 13 Synthesis of fully-modified 5′-[2′-O-methoxyethyl(TTT-TTT-TTT-TTT-TTT-TT)-3′ phosphorothioate 20-mer <Seq. ID No. 10>

The synthesis of the above homo-pyrimidine sequence was performed on aPharmacia OligoPilot II synthesizer on an 180 μmole scale usingcyanoethyl phosphoramidite of5′-O-DMT-2′-O-methoxyethyl-5-methyluridine. Pharmacia's HL 30 primersupport loaded with 2′-O-methoxyethyl-5-methyluridine was used.Detritylation was performed using 3% dichloroacetic acid in toluene(volume/volume). Activation of phosphoramidite was done with a 0.22 Msolution of pyridinium trifluoroacetate and 0.11 M solution of1-methylimidazole. Sulfurization was performed using a 0.2 M solution ofphenylacetyl disulfide in acetonitrile:3-picoline (1:1 v/v) for 2minutes. At the end of synthesis, the support was treated with asolution of triethylamine:acetonitrile (1:1, v/v) for 12 hours, supportwashed with acetonitrile, oligo cleaved, and deprotected with 33%aqueous ammonium hydroxide at 55° C. for 12 hours, cooled, concentrated,and purified by reversed phase HPLC. All DMT fractions were combined,analyzed by capillary gel electrophoresis, detritylated, precipitatedand lyophilized to a powder. The stepwise sulfurization efficiency wasfound to 99.7% based on ³¹P NMR (D₂O).

EXAMPLE 14 Synthesis of fully-modified5′-[2′-O-methoxyethyl-(GCTGA]-d(TTA-GAG-AGA-G)-[2′-O-methoxyethyl-(GTCCC)-3′phosphorothioate 20-mer <Seq. ID No. 11>

The synthesis of the above sequence was performed on a PharmaciaOligoPilot II synthesizer on an 180 μmole scale using cyanoethylphosphoramidite of 2′-deoxyribonucleosides and 2′-O-methoxyethylsubstituted ribonucleosides. Pharmacia's HL 30 primer support loadedwith 2′-O-methoxyethyl-N4benzoyl-5-methylcytidine was used.Detritylation was performed using 3% dichloroacetic acid in toluene(volume/volume). Activation of phosphoramidite was done with a 0.45 Msolution of 1H-tetrazole in acetonitrile. Sulfurization was performedusing a 0.2 M solution of phenylacetyl disulfide inacetonitrile:3-picoline (1:1 v/v) for 2 minutes. At the end ofsynthesis, the support was treated with a solution oftriethylamine:acetonitrile (1:1, v/v) for 12 hours, support washed withacetonitrile, oligo cleaved, and deprotected with 33% aqueous ammoniumhydroxide at 55° C. for 12 hours, cooled, concentrated, and purified byreversed phase HPLC. All DMT fractions were combined, analyzed bycapillary gel electrophoresis, detritylayed, precipitated andlyophilized to a powder. The stepwise sulfurization efficiency was foundto 99.7% based on ³¹P NMR (D₂O).

EXAMPLE 15 Synthesis of fully-modified5′-[2′-O-methoxyethyl-(CTG]-d(AGT-CTG-TTT)-[2′-O-methoxyethyl-(TCC-ATT-CT)-3′phosphorothioate 20-mer <Seq. ID No. 12>

The synthesis of the above sequence was performed on a PharmaciaOligoPilot II synthesizer on a 172 μmole scale using cyanoethylphosphoramidite of 2′-deoxyribonucleosides and 2′-O-methoxyethylsubstituted ribonucleosides. Pharmacia's HL 30 primer support loadedwith 2′-O-methoxyethyl-5-methyluridine was used. Detritylation wasperformed using 3% dichloroacetic acid in toluene (volume/volume).Activation of phosphoramidite was done with a 0.45 M solution of1H-tetrazole in acetonitrile. Sulfurization was performed using a 0.2 Msolution of phenylacetyl disulfide in acetonitrile:3-picoline (1:1 v/v)for 2 minutes. At the end of synthesis, the support was treated with asolution of triethylamine:acetonitrile (1:1, v/v) for 12 hours, supportwashed with acetonitrile, oligo cleaved, and deprotected with 33%aqueous ammonium hydroxide at 55° C. for 12 hours, cooled, concentrated,and purified by reversed phase HPLC. All DMT fractions were combined,analyzed by capillary gel electrophoresis, detritylated, precipitatedand lyophilized to a powder. The stepwise sulfurization efficiency wasfound to 99.7% based on ³¹P NMR (D₂O).

EXAMPLE 16 Synthesis of fully-modified5′-[2′-O-methoxyethyl(GCTGA]-d(TTA-GAG-AGA-G)-[2′-O-methoxyethyl-(GTCCC)-3′phosphorothioate 20-mer <Seq. ID No. 11>

The synthesis of the above sequence was performed on a PharmaciaOligoProcess I Synthesizer on a 150 mmole scale using cyanoethylphosphoramidite of 2′-deoxyribonucleosides and 2′-O-methoxyethylsubstituted ribonucleosides. Pharmacia's HL 30 primer support loadedwith 2′-O-methoxyethyl-N4benzoyl-5-methylcytidine was used.Detritylation was performed using 3% dichloroacetic acid in toluene(volume/volume). Activation of phosphoramidite was done with a 0.45 Msolution of 1H-tetrazole in acetonitrile. Sulfurization was performedusing a 0.2 M solution of phenylacetyl disulfide inacetonitrile:3-picoline (1:1 v/v) for 2.2 minutes. At the end ofsynthesis, the support was treated with a solution oftriethylamine:acetonitrile (1:1, v/v) for 12 hours, support washed withacetonitrile, oligo cleaved, and deprotected with 33% aqueous anmnoniurnhydroxide at 55° C. for 12 hours, cooled, concentrated, and purified byreversed phase HPLC. The DMT-on peak was fractionated, analyzed bycapillary gel electrophoresis, combined, detritylated, precipitated andlyophilized to a powder. The stepwise sulfurization efficiency was foundto 99.75% based on ³¹P NMR (D₂O).

EXAMPLE 17 Synthesis of fully-modified5′-[2′-O-methoxyethyl-(CTG]-d(AGT-CTG-TTT)-[2′-O-methoxyethyl-(TCC-ATT-CT)-3′phosphorothioate 20-mer <Seq. ID No. 12>

The synthesis of the above sequence was performed on a PharmaciaOligoPilot II synthesizer on a 40 mmole scale using cyanoethylphosphoramidite of 2′-deoxyribonucleosides and 2′-O-methoxyethylsubstituted ribonucleosides. Pharmacia's HL 30 primer support loadedwith 2′-O-methoxyethyl-5-methyluridine was used. Detritylation wasperformed using 15% dichloroacetic acid in toluene (volume/volume).Activation of phosphoramidite was done with a 0.45 M solution of1H-tetrazole in acetonitrile. Sulfurization was performed using a 0.2 Msolution of phenylacetyl disulfide in acetonitrile:3-picoline (1:1 v/v)for 2.2 minutes. At the end of synthesis, the support was treated with asolution of triethylamine:acetonitrile (1:1, v/v) for 12 hours, supportwashed with acetonitrile, oligo cleaved, and deprotected with 33%aqueous ammonium hydroxide at 55° C. for 12 hours, cooled, concentrated,and purified by reversed phase HPLC. The DMT-on peak was fractionated,analyzed by capillary gel electrophoresis, combined, detritylated,precipitated and lyophilized to a powder. The stepwise sulfurizationefficiency was found to 99.7% based on ³¹P NMR (D₂O).

EXAMPLE 18 Synthesis of fully modified5′-d(TCC-CGC-CTG-TGA)-2′-O-methoxyethyl-(CAT-GCA-TT)-3′ phosphorothioate20-mer <Seq. ID No. 13>

The synthesis of the above sequence was performed on a Milligen 8800synthesizer on a 282 μmole scale using the cyanoethyl phosphoramiditesand Pharmacia's HL 30 primer support. Detritylation was performed using3% dichloroacetic acid in toluene (volume/volume). Sulfurization wasperformed using a 0.4 M solution of phenylacetyl disulfide inacetonitrile:3-picoline (1:1 v/v) for 4 minutes. At the end ofsynthesis, the support was treated with a solution oftriethylamine:acetonitrile (1:1, v/v) for 12 hours, support washed withacetonitrile, oligo cleaved, and deprotected with 33% aqueous ammoniumhydroxide at 55° C. for 12 hours, cooled, concentrated, and purified byreversed phase HPLC. The DMT-on peak was fractionated, analyzed bycapillary gel electrophoresis, combined, detritylated, precipitated andlyophilized to a powder.

EXAMPLE 19 Synthesis of fully-modified5′-[2′-O-methoxyethyl-(GCTGA]-dTTA-GAG-AGA-G)-[2′-O-methoxyethyl-(GTCCC)-3′phosphorothioate 20-mer <Seq. ID No. 11>

The synthesis of the above sequence was performed on a PharmaciaOligoPilot II synthesizer on a 180 μmole scale using cyanoethylphosphoramidite of 2′-deoxyribonucleosides and 2′-O-methoxyethylsubstituted ribonucleosides. Pharmacia's HL 30 primer support loadedwith 2′-O-methoxyethyl-N4-benzoyl-5-methylcytidine was used.Detritylation was performed using 3% dichloroacetic acid in toluene(volume/volume). Activation of phosphoramidite was done with a 0.22 Msolution of pyridinium trifluoroacetate and 0.11 M solution of1-methylimidazole. Sulfurization was performed using a 0.2 M solution ofphenylacetyl disulfide in acetonitrile:3-picoline (1:1 v/v) for 2minutes. At the end of synthesis, the support was treated with asolution of triethylamine:acetonitrile (1:1, v/v) for 12 hours, supportwashed with acetonitrile, oligo cleaved, and deprotected with 33%aqueous ammonium hydroxide at 55° C. for 12 hours, cooled, concentrated,and purified by reversed phase HPLC. All DMT fractions were combined,analyzed by capillary gel electrophoresis, detritylated, precipitatedand lyophilized to a powder.

EXAMPLE 20 Synthesis of fully modified5′-[2′-methoxyethyl-(CTG]-d(AGT-CTG-TTT)-[2′-methoxyethyl-(TCC-ATT-CT)-3′phosphorothioate 20-mer <Seq. ID No. 12>

The synthesis of the above sequence was performed on a PharmaciaOligoPilot II synthesizer on a 172 μmole scale using cyanoethylphosphoramidite of 2′-deoxyribonucleosides and 2′-O-methoxyethylsubstituted ribonucleosides. Pharmacia's HL 30 primer support loadedwith 2′-O-methoxyethyl-5-methyluridine was used. Detritylation wasperformed using 3% dichloroacetic acid in toluene (volume/volume).Activation of phosphoramidite was done with a 0.22 M solution ofpyridinium trifluoroacetate and 0.11 M solution of 1-methylimidazole.Sulfurization was performed using a 0.2 M solution of phenylacetyldisulfide in acetonitrile:3-picoline (1:1 v/v) for 2 minutes. At the endof synthesis, the support was treated with a solution oftriethylamine:acetonitrile (1:1, v/v) for 12 hours, support washed withacetonitrile, oligo cleaved, and deprotected with 33% aqueous ammoniumhydroxide at 55° C. for 12 hours, cooled, concentrated, and purified byreversed phase HPLC. All DMT fractions were combined, analyzed bycapillary gel electrophoresis, detritylated, precipitated andlyophilized to a powder.

EXAMPLE 21 Synthesis of fully modified5′-d(GCC-CAA-GCT-GGC)-2′-O-methoxyethyl-(ATC-CGT-CA)-3′ phosphorothioate20-mer <Seq. ID No. 14>

The synthesis of the above sequence was performed on a Milligen 8800synthesizer on a 282 μmole scale using the cyanoethyl phosphoramiditesand Pharmacia's HL 30 primer support. Detritylation was performed using3% dichloroacetic acid in toluene (volume/volume). Sulfurization wasperformed using a 0.4 M solution of phenylacetyl disulfide inacetonitrile:3-picoline (1:1 v/v) for 4 minutes. At the end ofsynthesis, the support was treated with a solution oftriethylamine:acetonitrile (1:1, v/v) for 12 hours, support washed withacetonitrile, oligo cleaved, and deprotected with 33% aqueous ammoniumhydroxide at 55° C. for 12 hours, cooled, concentrated, and purified byreversed phase HPLC. The DMT-on peak was fractionated, analyzed bycapillary gel electrophoresis, combined, detritylated, precipitated andlyophilized to a powder.

EXAMPLE 22 Synthesis of fully-modified5′-[2′-O-methyl-(TTT-TTT-TTT-TTT-TTT-TTT-TT)-3′ phosphorothioate 20-mer<Seq. ID No. 15>

The synthesis of the above homo-pyrimidine sequence was performed on aPharmacia OligoPilot II synthesizer on a 180 μmole scale usingcyanoethyl phosphoramidite of 5′-O-DMT-2′-O-methyl-5-methyluridine.Pharmacia's HL 30 primer support loaded with 2′-O-methyl-5-methyluridinewas used. Detritylation was performed using 3% dichioroacetic acid intoluene (volume/volume). Activation of phosphoramidite was done with a0.45 M solution of 1H-tetrazole in acetonitrile. Sulfurization wasperformed using a 0.2 M solution of phenylacetyl disulfide inacetonitrile:3-picoline (1:1 v/v) for 2 minutes. At the end ofsynthesis, the support was treated with a solution oftriethylamine:acetonitrile (1:1, v/v) for 12 hours, support washed withacetonitrile, oligo cleaved, and deprotected with 33% aqueous ammoniumhydroxide at 55° C. for 12 hours, cooled, concentrated, and purified byreversed phase HPLC. All DMT fractions were combined, analyzed bycapillary, gel electrophoresis, detritylated, precipitated andlyophilized to a powder.

EXAMPLE 23 Synthesis of fully-modified5′-[2′-O-methyl-(TTT-TTT-TTT-TTT-TTT-TTT-TT)-3′ phosphorothioate 20-mer<Seq. ID No. 15>

The synthesis of the above homo-pyrimidine sequence was performed on aPharmacia OligoPilot II synthesizer on a 180 μmole scale usingcyanoethyl phosphoramidite of 5′-O-DMT-2′-O-methyl-5-methyluridine.Pharmacia's HL 30 primer support loaded with 2′-O-methyl-5-methyluridinewas used. Detritylation was performed using 3% dichloroacetic acid intoluene (volume/volume). Activation of phosphoramidite was done with a0.22 M solution of pyridinium trifluoroacetate and 0.11 M solution of1-methylimidazole. Sulfurization was performed using a 0.2 M solution ofphenylacetyl disulfide in acetonitrile:3-picoline (1:1 v/v) for 2minutes. At the end of synthesis, the support was treated with asolution of triethylamine:acetonitrile (1:1, v/v) for 12 hours, supportwashed with acetonitrile, oligo cleaved, and deprotected with 33%aqueous ammonium hydroxide at 55° C. for 12 hours, cooled, concentrated,and purified by reversed phase HPLC. All DMT fractions were combined,analyzed by capillary gel electrophoresis, detritylated, precipitatedand lyophilized to a powder.

EXAMPLE 24 Synthesis of fully-modified5′-[2′-O-methyl-(GCTGA]-d(TTA-GAG-AGA-G)-[2′-O-methyl-(GTCCC)-3′phosphorothioate 20-mer <Seq. ID No. 16>

The synthesis of the above sequence was performed on a PharmaciaOligoPilot II synthesizer on a 180 μmole scale using cyanoethylphosphoramidite of 2′-deoxyribonucleosides and 2′-O-methyl substitutedribonucleosides. Pharmacia's HL 30 primer support loaded with2′-O-methyl-N4-benzoyl-5-methylcytidine was used. Detritylation wasperformed using 3% dichloroacetic acid in toluene (volume/volume).Activation of phosphoramidite was done with a 0.45 M solution of1H-tetrazole in acetonitrile. Sulfurization was performed using a 0.2 Msolution of phenylacetyl disulfide in acetonitrile:3-picoline (1:1 v/v)for 2 minutes. At the end of synthesis, the support was treated with asolution of triethylamine:acetonitrile (1:1, v/v) for 12 hours, supportwashed with acetonitrile, oligo cleaved, and deprotected with 33%aqueous ammonium hydroxide at 55° C. for 12 hours, cooled, concentrated,and purified by reversed phase HPLC. All DMT fractions were combined,analyzed by capillary gel electrophoresis, detritylated, precipitatedand lyophilized to a powder. The stepwise sulfurization efficiency wasfound to 99.5% based on ³¹P NMR (D₂O).

Those skilled in the art will appreciate that numerous changes andmodifications may be made to the preferred embodiments of the inventionand that such changes and modifications may be made without departingfrom the spirit of the invention. It is therefore intended that theappended claims cover all such equivalent variations as fall within thetrue spirit and scope of the invention.

Various modifications of the invention, in addition to those describedherein, will be apparent to those skilled in the art from the foregoingdescription. Such modifications are intended to fall within the scope ofthe appended claims.

1. A method for preparing an oligonucleotide having at least onephosphorothioate internucleoside linkage, said method comprising:phosphitylating the 5′-hydroxyl of a nucleic acid moiety in anacetonitrile-containing solvent system to form a phosphite intermediate,said nucleic acid moiety being bound to a solid support; and oxidizingsaid phosphite intermediate with phenylacetyl disulfide in an aproticsolvent mixture including said acetonitrile-containing solvent systemand a basic solvent for a time sufficient to effect said conversion ofsaid phosphite intermediate to said phosphorothioate.
 2. The method ofclaim 1, wherein the oligonucleotide is between 8 nucleotides and 30nucleotides in length.
 3. The method of claim 1, wherein the aproticsolvent mixture includes a basic solvent selected from pyridine andhindered pyridines.
 4. The method of claim 1, wherein saidoligonucleotide comprises at least one 2′-modified nucleoside.
 5. Themethod of claim 1, wherein said oligonucleotide comprises at least onedeoxynucleoside.
 6. The method of claim 3, wherein the hindered pyridineis a collidine, a picoline or a lutidine.
 7. The method of claim 6,wherein said picoline is 3-picoline.
 8. The method of claim 1, whereinsaid phosphite intermediate is a dinucleotide phosphite.
 9. The methodof claim 1, wherein said phosphitylating is performed with aphosphoramidite.